BioC 2.12: CHECK report for ENVISIONQuery on moscato2

Package: ENVISIONQuery

Version: 1.7.0

Command: rm -rf ENVISIONQuery.buildbin-libdir && mkdir ENVISIONQuery.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.7.0.tar.gz >ENVISIONQuery-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=ENVISIONQuery.buildbin-libdir --install="check:ENVISIONQuery-install.out" --force-multiarch --no-vignettes --timings ENVISIONQuery_1.7.0.tar.gz && mv ENVISIONQuery.buildbin-libdir/* ENVISIONQuery.Rcheck/ && rmdir ENVISIONQuery.buildbin-libdir

StartedAt: 2013-03-25 02:13:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:15:09 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 78.5 seconds

RetCode: 0

Status: OK

CheckDir: ENVISIONQuery.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENVISIONQuery' version '1.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ENVISIONQuery' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'ENVISIONQuery/R/zzz.R':
  .onAttach calls:
    cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'ENVISIONQuery.lyx'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [17s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ENVISIONQuery 2.76   0.54   15.24
** running examples for arch 'x64' ... [16s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ENVISIONQuery  3.4   0.08   14.29
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ENVISIONQuery' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ENVISIONQuery.Rnw' using 'latin-9' 
** testing if installed package can be loaded
This is  ENVISIONQuery   1.7.0   2011-07-17 

install for x64

* installing *source* package 'ENVISIONQuery' ...
** testing if installed package can be loaded
This is  ENVISIONQuery   1.7.0   2011-07-17 
* MD5 sums
packaged installation of 'ENVISIONQuery' as ENVISIONQuery_1.7.0.zip
* DONE (ENVISIONQuery)

Summary

Command output